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Tuesday, 29 July 2014

I wrote at the weekend about the new Y Prime test from Full Genomes which is designed as a competitor to Family Tree DNA's Big Y test. Family Tree DNA have now responded by announcing a permanent reduction in the price of their Big Y test, and they have also introduced a few new features to the Big Y display. Note that FTDNA's Big Y is only available to existing FTDNA customers. It's good to see some healthy competition in the Y-DNA testing market. Here is the text of the e-mail that was sent out to project administrators:

Dear
Project Administrators,

We are excited to announce the release of a new
feature to help Big Y testers refine their matches! Now, you'll be able to
easily filter out matches that aren't genealogically relevant to
you.

Also, as part of this release we are permanently reducing the price
of Big
Y to $595.

How it
Works

The
filter lists the subclades immediately upstream from the tester's terminal
subclade. When a subclade has been selected, a number appears next to the
unselected subclades to indicate how far upstream or downstream they are from
the selected subclade.

A subclade marked (+1) is the next clade
upstream from the currently selected clade. A subclade marked (-1) is the next
clade downstream from the currently selected clade. The number of matches
available at each level is listed on the right side of the filter drop
down.

To
help clarify the hierarchy of the subclades, the haplotree button has been
updated to display subclades in the standard haplotree format. The full tree can be viewed by clicking Go To
Haplotree.

FGC has worked with industry leaders to develop a new Y chromosome capture approach and has combined it with Illumina "next-gen" sequencing. The resulting data will be processed with the latest alignment algorithms to improve read mapping. The overall result is a cutting-edge product with Y chromosome coverage breadth that is close to that of FGC's original comprehensive Y sequencing product (now termed Y Elite), at a much lower cost. Additionally, the new product is priced lower than the leading competitor, while retaining a significant advantage in terms of quality and comprehensiveness.

FGC is releasing the following comparison statistics as estimates of test coverage based on Y Prime pilot results.

Y Prime will be offered at a standard price of $625. An introductory price of $599 is available for orders placed by August 31, 2014. Y Prime is currently available at the discounted introductory price through the Full Genomes website by ordering the Comprehensive Y test using the coupon code "YPRIME".

The new product is also expected to offer significant improvements in turnaround time for results. Testing will be performed by a U.S.-based sequencing facility.

Additionally, FGC has recently been developing new sample collection protocols, designed to reduce the frequency of delays due to the need for repeat sample collection.

Justin Loe, CEO of FGC, commented, "Our new product is consistent with our mission to deliver the best quality Y sequencing products at the most affordable prices possible, and to continue to innovate with new products targeted to the genetic genealogy community."

FGC will continue to offer the original comprehensive Y sequencing product, with sequencing performed at BGI, under the new name Y Elite. To help customers decide which product is right for them, FGC is releasing BED files to indicate the regions covered by representative tests; these are available at http://goo.gl/pcq6FE and can be used to determine whether a particular site or SNP of interest is likely to be covered by the test. Customers with questions may contact orders@fullgenomes.com.

DAK note: I am advised that Greg Magoon has further technical comparisons available, which are the raw
data files from the pilot samples (BAM files and FGC analytical reports), that are also available for
comparison for specialists.Update 29 July 2014
Full Genomes have announced that the Y Prime test will be offered at a new low price of $589.

Friday, 25 July 2014

The August 2014 issue of Family Tree Magazine includes a letter I wrote in response to two stories in their July issue which claimed that it is possible to identify someone's "genetic homeland" from a DNA test. There was not space in the magazine to include the full text of my letter and the editor has kindly given me permission to reproduce the full letter here.

In your July issue you published two articles which claimed to show that it is possible to pinpoint your "genetic homeland" a thousand or more years ago by taking a simple DNA test. It would indeed be wonderful if a DNA test could give us this information but sadly it is not possible.

The first story “DNA: find your ancestral home” (p9) referred to a new autosomal DNA test developed by a company called Prosapia Genetics. They claim that they are able to pinpoint someone’s genetic homeland one thousand years ago and that their test is “accurate to home village with a time resolution of the past 1,000 years”. The underlying research on which this test is based was published in a scientific journal (Elhaik et el 2014, Nature Communications 5: 3513). However, the researchers were only able to place 50% of people within 450 kilometres of their country of origin, which is hardly the level of precision claimed. Furthermore the research focused solely on the present-day country of origin and made no attempt to determine an ancestral origin one thousand years ago. Such a method is best thought of as human provenancing – finding the location where an individual’s genotype is most likely to be found – not a method for inferring ancestry. Indeed, if you go back one thousand years you have in theory about 35 billion ancestors, although you actually inherited DNA from only a small, random subset of those ancestors. Identifying a single location as the “genetic homeland” of either all your pedigree ancestors or just the DNA ancestors would be a meaningless exercise. The International Society of Genetic Genealogy received a number of reports from dissatisfied customers of Prosapia Genetics, many of whom had received bizarre results placing their "genetic homeland" in the middle of a river or ocean. Fortunately they were able to get refunds from PayPal.

Dr Tyrone Bowes, the author of the second article "Routes to roots" (pp14-18), claims to be able to tell his customers when their ancestors arrived in Britain and where they came from based on recurring surname matches received as part of a commercial Y-chromosome DNA test. DNA testing is a very useful tool for the genealogist, and Y-DNA matches can often provide clues about our recent origins. However, Y-DNA results should always be interpreted in combination with genealogical and historical records. While a Y-DNA test is very good at indicating whether or not two people share a recent male-line ancestor, it is much more difficult to determine precisely when or where that ancestor might have lived. For example, a match on 34 out of 37 markers could indicate a shared ancestor who lived 200 years ago or 2000 years ago, and there is no way of determining the precise timeframe. Furthermore, surnames did not become common in Britain one thousand years ago, as is claimed. They were introduced into Britain with the Norman Conquest but the adoption of surnames was a gradual process. While most English people had acquired surnames by the fifteenth century, surnames were not adopted until the nineteenth century in some parts of Wales. In the Highlands of Scotland the clan system survived until the eighteenth century, and people adopted the name of the clan rather than using an hereditary surname. Even when surnames are passed on through the fatherline the link between the Y-chromosome and the surname is often broken as a result of illegitimacy, cuckoldry, adoption or name changes. In addition, there is an inherent American bias in the commercial databases. Consequently Y-DNA matches will often tell us more about non-paternity events in Colonial America in the last 400 years, rather than a person’s origins in the British Isles. All these factors need to be taken into account when interpreting DNA results.

The mutations that determine haplogroups (the deep-rooted branches of the human Y-DNA tree) did indeed occur at a specific time and place several thousand years ago, but determining when and where that happened is a different matter entirely. We are reliant on making inferences from the DNA of living people. However, the current distribution of haplogroups differs from each of the distributions at different times in the past. The changes occur due to migration and the randomness of genetic drift. As more ancient DNA samples become available it might one day be possible to provide some answers, but we are not there yet and it is unlikely that we will ever be able to "precisely reconstruct our ancestral journey".

Readers wishing to understand more about the legitimate uses of DNA testing for genealogy and the limited inferences that can be made from deep ancestry tests might like to refer to the new “Debunking genetic astrology” website that I have worked on with my colleagues at University College London: www.ucl.ac.uk/mace-lab/debunking. In particular readers might like to look at the page on dubious commercial claims (www.ucl.ac.uk/mace-lab/debunking/companies) where the genetic homeland stories are discussed in greater detail.

The editor also included in the August issue of Family Tree Magazine responses to my letter from Vladimir Makarov of Prosapia Genetics and Tyrone Bowes, the creator of the Irish, Scottish and English Origenes websites. Unfortunately, neither letter addressed any of the issues I'd raised. Vladimir Makarov argued that his reports do reflect ancient origins simply because the reference populations he uses are "totally agnostic of political boundaries". He failed to recognise that these reference populations are themselves possibly admixed and do not necessarily represent the population in the same location one thousand years ago. Tyrone Bowes went into great detail about a case report that he'd compiled for a Mr Valentine which purported to show a link with the McGregors. It seems that his entire dating method has been based on this single case. Numerous scientific studies have of course demonstrated that mutations occur at random, and any attempt to investigate the validity of matches must take into account the uncertainties in the TMRCA (time to the most recent common ancestor) calculations. My points about differing times of surname adoption and non-paternity events remained unanswered.

For further information about Prosapia Genetics and the case reports offered by the Irish, Scottish and English Origenes websites see my two earlier blog posts:

The aim of the website is to explain how genetic ancestry tests work and to explain what such tests can and can't tell you, but with a particular focus on the inferences made about our deep ancestry. I am a passionate advocate for the use of DNA testing for genealogical purposes. DNA can be a very powerful tool when used in combination with both genealogical and historical records, especially now that the genetic genealogy databases are so large. However, it is much more difficult to make inferences about deep ancestry based on DNA evidence alone. Unfortunately many misleading stories and dubious claims which are not supported by the scientific evidence have appeared in the media. Such "genetic astrology" stories only serve to undermine public confidence in DNA testing and prevent the subject from being taken seriously. It is often difficult for the uninformed reader to make sense of these stories and to separate the facts from the storytelling. We hope that our website will go some way to setting the record straight.

Saturday, 12 July 2014

A number of newspapers this week, including The Independent, the Sunday Telegraph, the Daily Mail and the Huffington Post, reported on a ludicrous story suggesting that the gene associated with red hair could die out as a result of climate change. The source of this story appears to be an interview with "DNA expert... Dr Alistair Moffat, boss of genetic testing company ScotlandsDNA" published in the Scottish Daily Record. I have not been able to find any evidence that Alistair Moffat has a PhD in any subject and he does not seem to have any qualifications in genetics so it is somewhat surprising to find that he is described both as a doctor and as a DNA expert. Most unusually the story was supported by a quote from "another scientist, who asked not to be named because of the theoretical nature of the work". I do not ever recall seeing any story in the press before where a scientist insisted on retaining his or her anonymity, though it is perhaps understandable in view of the nonsensical nature of the theory.

ScotlandsDNA have since claimed that Alistair Moffat was misquoted, though they have not enlightened us as to what exactly Alistair Moffat is supposed to have said.

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The material on these pages is copyright Debbie Kennett or reproduced with permission from other copyright owners. It may be downloaded and printed for personal reference, but not otherwise copied, altered in any way or transmitted to others (unless explicitly stated otherwise) without the written permission of Debbie Kennett.